Multiple sequence alignment - TraesCS3B01G297000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G297000 chr3B 100.000 5395 0 0 1 5395 476045952 476040558 0.000000e+00 9963
1 TraesCS3B01G297000 chr3B 94.525 621 32 2 1 621 306063027 306062409 0.000000e+00 957
2 TraesCS3B01G297000 chr3B 93.851 618 38 0 1 618 306768696 306769313 0.000000e+00 931
3 TraesCS3B01G297000 chr3A 93.943 4606 140 43 873 5395 487452056 487447507 0.000000e+00 6831
4 TraesCS3B01G297000 chr3A 89.189 185 15 5 694 875 487452335 487452153 5.440000e-55 226
5 TraesCS3B01G297000 chr3D 96.131 2869 93 10 809 3661 365537051 365534185 0.000000e+00 4667
6 TraesCS3B01G297000 chr3D 93.302 1687 68 11 3740 5395 365534120 365532448 0.000000e+00 2447
7 TraesCS3B01G297000 chr5B 94.212 622 35 1 1 621 144672383 144673004 0.000000e+00 948
8 TraesCS3B01G297000 chr1B 94.042 621 36 1 1 621 529736629 529736010 0.000000e+00 941
9 TraesCS3B01G297000 chr1B 93.538 619 37 3 1 618 251775595 251774979 0.000000e+00 918
10 TraesCS3B01G297000 chr5D 93.689 618 39 0 1 618 392089603 392088986 0.000000e+00 926
11 TraesCS3B01G297000 chr4D 93.538 619 40 0 1 619 417146278 417146896 0.000000e+00 922
12 TraesCS3B01G297000 chr7B 93.528 618 40 0 4 621 437988548 437989165 0.000000e+00 920
13 TraesCS3B01G297000 chr6B 93.528 618 40 0 1 618 399759132 399759749 0.000000e+00 920


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G297000 chr3B 476040558 476045952 5394 True 9963.0 9963 100.0000 1 5395 1 chr3B.!!$R2 5394
1 TraesCS3B01G297000 chr3B 306062409 306063027 618 True 957.0 957 94.5250 1 621 1 chr3B.!!$R1 620
2 TraesCS3B01G297000 chr3B 306768696 306769313 617 False 931.0 931 93.8510 1 618 1 chr3B.!!$F1 617
3 TraesCS3B01G297000 chr3A 487447507 487452335 4828 True 3528.5 6831 91.5660 694 5395 2 chr3A.!!$R1 4701
4 TraesCS3B01G297000 chr3D 365532448 365537051 4603 True 3557.0 4667 94.7165 809 5395 2 chr3D.!!$R1 4586
5 TraesCS3B01G297000 chr5B 144672383 144673004 621 False 948.0 948 94.2120 1 621 1 chr5B.!!$F1 620
6 TraesCS3B01G297000 chr1B 529736010 529736629 619 True 941.0 941 94.0420 1 621 1 chr1B.!!$R2 620
7 TraesCS3B01G297000 chr1B 251774979 251775595 616 True 918.0 918 93.5380 1 618 1 chr1B.!!$R1 617
8 TraesCS3B01G297000 chr5D 392088986 392089603 617 True 926.0 926 93.6890 1 618 1 chr5D.!!$R1 617
9 TraesCS3B01G297000 chr4D 417146278 417146896 618 False 922.0 922 93.5380 1 619 1 chr4D.!!$F1 618
10 TraesCS3B01G297000 chr7B 437988548 437989165 617 False 920.0 920 93.5280 4 621 1 chr7B.!!$F1 617
11 TraesCS3B01G297000 chr6B 399759132 399759749 617 False 920.0 920 93.5280 1 618 1 chr6B.!!$F1 617

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
51 52 0.036671 ACGAAAATCTGTCCGGGGAC 60.037 55.0 10.95 10.95 44.77 4.46 F
627 630 0.391597 GACTCCCTCAACGTGTCCAA 59.608 55.0 0.00 0.00 0.00 3.53 F
640 643 0.753867 TGTCCAAACGCTCCTGTGTA 59.246 50.0 0.00 0.00 35.64 2.90 F
2001 2135 0.460987 GGAGAGTTGCCACCGATCAG 60.461 60.0 0.00 0.00 0.00 2.90 F
3679 3843 0.398381 GGGGGAATTGCAAGCCCATA 60.398 55.0 30.51 0.00 43.89 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1648 0.320421 TTCCCGTAAGCAGCAGTGAC 60.320 55.000 0.00 0.00 0.00 3.67 R
1982 2115 0.460987 CTGATCGGTGGCAACTCTCC 60.461 60.000 0.00 0.00 37.61 3.71 R
2125 2262 1.209747 CCCCTAAGCTTGACTGGTACC 59.790 57.143 9.86 4.43 0.00 3.34 R
3919 4086 0.613292 ATGTCAGCCAGGACTCGTCT 60.613 55.000 0.00 0.00 38.61 4.18 R
4763 4968 1.067295 TGTCACCCCTCATTGCTTCT 58.933 50.000 0.00 0.00 0.00 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.036671 ACGAAAATCTGTCCGGGGAC 60.037 55.000 10.95 10.95 44.77 4.46
63 64 1.213430 TCCGGGGACAAAAACTTCACT 59.787 47.619 0.00 0.00 0.00 3.41
104 105 3.008835 TGATTGAAGGAGCCATCAAGG 57.991 47.619 12.09 0.00 37.13 3.61
144 145 3.817647 GTGGAACTCTCAATGAAAGCACT 59.182 43.478 0.00 0.00 0.00 4.40
184 185 0.398664 CGGATCTCAGGTAGGGGGTT 60.399 60.000 0.00 0.00 0.00 4.11
208 209 3.323243 GAACTGTGCGTCTAAGGCTAAA 58.677 45.455 0.00 0.00 0.00 1.85
244 245 2.224917 GGGGACACAATGTTTACCCAGA 60.225 50.000 14.80 0.00 38.30 3.86
459 462 4.023107 CACAGAGTCGGTTACAGAGAAAGA 60.023 45.833 0.00 0.00 0.00 2.52
555 558 8.802267 GTCTTCTATCTTGTATCTTCATAGCCT 58.198 37.037 0.00 0.00 0.00 4.58
579 582 4.748892 ACAGTCCGACATATGCATATAGC 58.251 43.478 18.70 12.29 45.96 2.97
584 587 2.100749 CGACATATGCATATAGCCCGGA 59.899 50.000 18.70 0.00 44.83 5.14
621 624 2.800159 ATCCGGGACTCCCTCAACGT 62.800 60.000 12.62 0.00 42.67 3.99
622 625 2.261671 CGGGACTCCCTCAACGTG 59.738 66.667 12.62 0.00 42.67 4.49
623 626 2.571216 CGGGACTCCCTCAACGTGT 61.571 63.158 12.62 0.00 42.67 4.49
624 627 1.292541 GGGACTCCCTCAACGTGTC 59.707 63.158 6.90 0.00 41.34 3.67
625 628 1.292541 GGACTCCCTCAACGTGTCC 59.707 63.158 3.53 3.53 40.05 4.02
626 629 1.469335 GGACTCCCTCAACGTGTCCA 61.469 60.000 12.64 0.00 44.59 4.02
627 630 0.391597 GACTCCCTCAACGTGTCCAA 59.608 55.000 0.00 0.00 0.00 3.53
628 631 0.834612 ACTCCCTCAACGTGTCCAAA 59.165 50.000 0.00 0.00 0.00 3.28
629 632 1.226746 CTCCCTCAACGTGTCCAAAC 58.773 55.000 0.00 0.00 0.00 2.93
636 639 3.244105 CGTGTCCAAACGCTCCTG 58.756 61.111 0.00 0.00 36.65 3.86
637 640 1.594293 CGTGTCCAAACGCTCCTGT 60.594 57.895 0.00 0.00 36.65 4.00
638 641 1.831389 CGTGTCCAAACGCTCCTGTG 61.831 60.000 0.00 0.00 36.65 3.66
639 642 0.814010 GTGTCCAAACGCTCCTGTGT 60.814 55.000 0.00 0.00 38.76 3.72
640 643 0.753867 TGTCCAAACGCTCCTGTGTA 59.246 50.000 0.00 0.00 35.64 2.90
641 644 1.346395 TGTCCAAACGCTCCTGTGTAT 59.654 47.619 0.00 0.00 35.64 2.29
642 645 1.732259 GTCCAAACGCTCCTGTGTATG 59.268 52.381 0.00 0.00 35.64 2.39
643 646 1.346395 TCCAAACGCTCCTGTGTATGT 59.654 47.619 0.00 0.00 35.64 2.29
644 647 2.151202 CCAAACGCTCCTGTGTATGTT 58.849 47.619 0.00 0.00 35.64 2.71
645 648 2.552315 CCAAACGCTCCTGTGTATGTTT 59.448 45.455 0.00 0.00 35.64 2.83
646 649 3.749088 CCAAACGCTCCTGTGTATGTTTA 59.251 43.478 0.00 0.00 35.64 2.01
647 650 4.142902 CCAAACGCTCCTGTGTATGTTTAG 60.143 45.833 0.00 0.00 35.64 1.85
648 651 3.247006 ACGCTCCTGTGTATGTTTAGG 57.753 47.619 0.00 0.00 34.82 2.69
649 652 2.093658 ACGCTCCTGTGTATGTTTAGGG 60.094 50.000 0.00 0.00 34.82 3.53
650 653 2.741878 CGCTCCTGTGTATGTTTAGGGG 60.742 54.545 0.00 0.00 33.82 4.79
651 654 2.504175 GCTCCTGTGTATGTTTAGGGGA 59.496 50.000 0.00 0.00 32.33 4.81
652 655 3.136626 GCTCCTGTGTATGTTTAGGGGAT 59.863 47.826 0.00 0.00 32.33 3.85
653 656 4.708177 CTCCTGTGTATGTTTAGGGGATG 58.292 47.826 0.00 0.00 32.33 3.51
654 657 3.458118 TCCTGTGTATGTTTAGGGGATGG 59.542 47.826 0.00 0.00 0.00 3.51
655 658 3.458118 CCTGTGTATGTTTAGGGGATGGA 59.542 47.826 0.00 0.00 0.00 3.41
656 659 4.104738 CCTGTGTATGTTTAGGGGATGGAT 59.895 45.833 0.00 0.00 0.00 3.41
657 660 5.399038 CCTGTGTATGTTTAGGGGATGGATT 60.399 44.000 0.00 0.00 0.00 3.01
658 661 6.086011 TGTGTATGTTTAGGGGATGGATTT 57.914 37.500 0.00 0.00 0.00 2.17
659 662 5.890985 TGTGTATGTTTAGGGGATGGATTTG 59.109 40.000 0.00 0.00 0.00 2.32
660 663 4.892934 TGTATGTTTAGGGGATGGATTTGC 59.107 41.667 0.00 0.00 0.00 3.68
661 664 3.464720 TGTTTAGGGGATGGATTTGCA 57.535 42.857 0.00 0.00 0.00 4.08
662 665 3.784178 TGTTTAGGGGATGGATTTGCAA 58.216 40.909 0.00 0.00 0.00 4.08
663 666 4.163427 TGTTTAGGGGATGGATTTGCAAA 58.837 39.130 15.44 15.44 0.00 3.68
664 667 4.222588 TGTTTAGGGGATGGATTTGCAAAG 59.777 41.667 18.19 0.00 0.00 2.77
665 668 2.629017 AGGGGATGGATTTGCAAAGT 57.371 45.000 18.19 5.95 0.00 2.66
666 669 2.460669 AGGGGATGGATTTGCAAAGTC 58.539 47.619 18.19 13.97 0.00 3.01
667 670 2.043526 AGGGGATGGATTTGCAAAGTCT 59.956 45.455 18.19 0.04 32.53 3.24
668 671 2.167075 GGGGATGGATTTGCAAAGTCTG 59.833 50.000 18.19 0.00 32.53 3.51
669 672 2.167075 GGGATGGATTTGCAAAGTCTGG 59.833 50.000 18.19 0.00 32.53 3.86
670 673 2.827921 GGATGGATTTGCAAAGTCTGGT 59.172 45.455 18.19 0.00 32.53 4.00
671 674 3.259123 GGATGGATTTGCAAAGTCTGGTT 59.741 43.478 18.19 0.00 32.53 3.67
672 675 3.731652 TGGATTTGCAAAGTCTGGTTG 57.268 42.857 18.19 0.00 32.53 3.77
673 676 3.030291 TGGATTTGCAAAGTCTGGTTGT 58.970 40.909 18.19 0.00 32.53 3.32
674 677 4.211125 TGGATTTGCAAAGTCTGGTTGTA 58.789 39.130 18.19 0.00 32.53 2.41
675 678 4.278170 TGGATTTGCAAAGTCTGGTTGTAG 59.722 41.667 18.19 0.00 32.53 2.74
676 679 4.518970 GGATTTGCAAAGTCTGGTTGTAGA 59.481 41.667 18.19 0.00 32.53 2.59
677 680 5.183904 GGATTTGCAAAGTCTGGTTGTAGAT 59.816 40.000 18.19 0.00 32.53 1.98
678 681 5.437289 TTTGCAAAGTCTGGTTGTAGATG 57.563 39.130 8.05 0.00 0.00 2.90
679 682 3.411446 TGCAAAGTCTGGTTGTAGATGG 58.589 45.455 0.00 0.00 0.00 3.51
680 683 2.162408 GCAAAGTCTGGTTGTAGATGGC 59.838 50.000 0.00 0.00 0.00 4.40
681 684 3.679389 CAAAGTCTGGTTGTAGATGGCT 58.321 45.455 0.00 0.00 0.00 4.75
682 685 4.832248 CAAAGTCTGGTTGTAGATGGCTA 58.168 43.478 0.00 0.00 0.00 3.93
683 686 5.245531 CAAAGTCTGGTTGTAGATGGCTAA 58.754 41.667 0.00 0.00 0.00 3.09
684 687 4.744795 AGTCTGGTTGTAGATGGCTAAG 57.255 45.455 0.00 0.00 0.00 2.18
685 688 4.097418 AGTCTGGTTGTAGATGGCTAAGT 58.903 43.478 0.00 0.00 0.00 2.24
686 689 5.269991 AGTCTGGTTGTAGATGGCTAAGTA 58.730 41.667 0.00 0.00 0.00 2.24
687 690 5.361285 AGTCTGGTTGTAGATGGCTAAGTAG 59.639 44.000 0.00 0.00 0.00 2.57
688 691 5.127356 GTCTGGTTGTAGATGGCTAAGTAGT 59.873 44.000 0.00 0.00 0.00 2.73
689 692 5.720041 TCTGGTTGTAGATGGCTAAGTAGTT 59.280 40.000 0.00 0.00 0.00 2.24
690 693 5.730550 TGGTTGTAGATGGCTAAGTAGTTG 58.269 41.667 0.00 0.00 0.00 3.16
691 694 5.247564 TGGTTGTAGATGGCTAAGTAGTTGT 59.752 40.000 0.00 0.00 0.00 3.32
692 695 6.438108 TGGTTGTAGATGGCTAAGTAGTTGTA 59.562 38.462 0.00 0.00 0.00 2.41
693 696 7.125204 TGGTTGTAGATGGCTAAGTAGTTGTAT 59.875 37.037 0.00 0.00 0.00 2.29
694 697 7.985752 GGTTGTAGATGGCTAAGTAGTTGTATT 59.014 37.037 0.00 0.00 0.00 1.89
695 698 9.379791 GTTGTAGATGGCTAAGTAGTTGTATTT 57.620 33.333 0.00 0.00 0.00 1.40
696 699 9.953565 TTGTAGATGGCTAAGTAGTTGTATTTT 57.046 29.630 0.00 0.00 0.00 1.82
697 700 9.953565 TGTAGATGGCTAAGTAGTTGTATTTTT 57.046 29.630 0.00 0.00 0.00 1.94
712 715 9.705290 AGTTGTATTTTTCTTTTGAAACACAGT 57.295 25.926 0.00 0.00 46.80 3.55
719 722 6.851222 TTCTTTTGAAACACAGTTGCAAAA 57.149 29.167 21.24 21.24 37.06 2.44
726 729 5.288232 TGAAACACAGTTGCAAAAGAAATCG 59.712 36.000 0.00 0.00 0.00 3.34
729 732 4.562394 ACACAGTTGCAAAAGAAATCGTTG 59.438 37.500 0.00 0.00 0.00 4.10
779 784 7.429340 GCAAATAGTCCACGTAGAAAAATCATG 59.571 37.037 0.00 0.00 0.00 3.07
783 788 5.639506 AGTCCACGTAGAAAAATCATGACAG 59.360 40.000 0.00 0.00 0.00 3.51
797 802 6.566079 ATCATGACAGTCTATCCTCCAAAA 57.434 37.500 0.00 0.00 0.00 2.44
806 811 7.181125 ACAGTCTATCCTCCAAAACTCATAAGT 59.819 37.037 0.00 0.00 37.32 2.24
807 812 7.493971 CAGTCTATCCTCCAAAACTCATAAGTG 59.506 40.741 0.00 0.00 35.36 3.16
1151 1261 2.357517 CGCAAACTCCCAGCGTCT 60.358 61.111 0.00 0.00 45.82 4.18
1519 1648 0.868406 GGTGAGACCAGAACTTTGCG 59.132 55.000 0.00 0.00 38.42 4.85
1566 1695 4.922206 TGCCACAGAGGTTTCTTGATATT 58.078 39.130 0.00 0.00 40.61 1.28
1572 1701 4.572389 CAGAGGTTTCTTGATATTCCACCG 59.428 45.833 0.00 0.00 0.00 4.94
1575 1704 3.181500 GGTTTCTTGATATTCCACCGTGC 60.181 47.826 0.00 0.00 0.00 5.34
1602 1731 4.892433 AGTCCAGAAATCTGTCTGTCAAG 58.108 43.478 9.43 0.00 43.02 3.02
1635 1764 5.982465 TGCCTTTGTTTTAGTTCAATTGC 57.018 34.783 0.00 0.00 0.00 3.56
1728 1857 5.878116 ACATTGGCTAGCGACTATTGTTTAA 59.122 36.000 9.00 0.00 0.00 1.52
1804 1933 4.219725 ACTTTGGTAGTTTTGTTGCAGTGT 59.780 37.500 0.00 0.00 31.29 3.55
1832 1961 5.930837 AACCAAATCAGGTCTTTTTGTGA 57.069 34.783 0.00 0.00 42.25 3.58
1932 2065 5.879223 CCCAAATATCCACTCATATCAGCTC 59.121 44.000 0.00 0.00 0.00 4.09
1979 2112 8.053776 TCATAGGACTAGGAGAACTAATGGTA 57.946 38.462 0.00 0.00 0.00 3.25
1980 2113 8.679725 TCATAGGACTAGGAGAACTAATGGTAT 58.320 37.037 0.00 0.00 0.00 2.73
1982 2115 6.005198 AGGACTAGGAGAACTAATGGTATCG 58.995 44.000 0.00 0.00 0.00 2.92
2001 2135 0.460987 GGAGAGTTGCCACCGATCAG 60.461 60.000 0.00 0.00 0.00 2.90
2017 2151 4.307443 GATCAGTCGATGTCCATACACA 57.693 45.455 0.00 0.00 38.78 3.72
2029 2163 7.441157 CGATGTCCATACACAACCATTATTAGT 59.559 37.037 0.00 0.00 38.78 2.24
2067 2201 9.815936 CAAATAATTTCAAATCAAGCTTTGTCC 57.184 29.630 0.00 0.00 37.39 4.02
2125 2262 1.164041 ACAAACCGAACTTCCAGCCG 61.164 55.000 0.00 0.00 0.00 5.52
2175 2312 2.263895 ACTAACCATACCCTGCCAGA 57.736 50.000 0.00 0.00 0.00 3.86
2189 2326 3.511146 CCTGCCAGAAAACAATATGTGGT 59.489 43.478 0.00 0.00 32.77 4.16
2248 2385 5.010012 ACTTTGAACCCTGATCATTTGTCAC 59.990 40.000 0.00 0.00 0.00 3.67
2271 2408 4.400251 CGTCTCCTTGTATACCAGGTACAA 59.600 45.833 19.66 4.54 39.12 2.41
2359 2497 4.094887 GGTTGTATGATGCACCTGTTACAG 59.905 45.833 5.22 5.22 0.00 2.74
2379 2517 5.564550 ACAGTTCTGAGCCAGTCAAATTAT 58.435 37.500 6.83 0.00 33.60 1.28
2648 2787 9.177608 TGTGCTGATGCTAATAGTTAGAAAAAT 57.822 29.630 1.10 0.00 40.48 1.82
2671 2810 1.208052 AGGCTTCTCGCTTGCTATTCA 59.792 47.619 0.00 0.00 39.13 2.57
2679 2818 7.532209 GCTTCTCGCTTGCTATTCATTATAAAC 59.468 37.037 0.00 0.00 35.14 2.01
2702 2841 5.932303 ACTATAACCATCATTTCGGGATTCG 59.068 40.000 0.00 0.00 40.90 3.34
2776 2915 6.456988 GCACTATCATACTTTTAGTGTGGTGC 60.457 42.308 14.99 14.99 41.50 5.01
2847 2988 5.693104 GCACCATATTTAAACTGGCATGATG 59.307 40.000 15.37 9.05 33.12 3.07
2882 3023 7.408756 TTGCTAATTTACTGGATGATGCTTT 57.591 32.000 0.00 0.00 0.00 3.51
3163 3304 9.010029 CCTCTCCTAGATAGACTTGATTAGTTC 57.990 40.741 0.00 0.00 37.17 3.01
3195 3336 6.861065 TTACAATTCACAGAGAAACAGGTC 57.139 37.500 0.00 0.00 40.22 3.85
3207 3348 8.718734 ACAGAGAAACAGGTCGAATATTTTAAC 58.281 33.333 0.00 0.00 0.00 2.01
3208 3349 7.898309 CAGAGAAACAGGTCGAATATTTTAACG 59.102 37.037 0.00 0.00 0.00 3.18
3355 3496 3.369147 CACAAGATGACTCCAAAGCTACG 59.631 47.826 0.00 0.00 0.00 3.51
3470 3618 4.154942 TGGGTATAGAATTCCTCGGTACC 58.845 47.826 0.16 0.16 37.81 3.34
3494 3642 6.486657 CCAGTCTTTGTCAAAATTCACTAGGA 59.513 38.462 0.00 0.00 0.00 2.94
3621 3769 2.541346 AGTTCATATGCGATGACTTGCG 59.459 45.455 0.00 0.00 34.16 4.85
3679 3843 0.398381 GGGGGAATTGCAAGCCCATA 60.398 55.000 30.51 0.00 43.89 2.74
3700 3864 6.239204 CCATATGTTGCATTCACCTGATCATT 60.239 38.462 0.00 0.00 0.00 2.57
3701 3865 7.040271 CCATATGTTGCATTCACCTGATCATTA 60.040 37.037 0.00 0.00 0.00 1.90
3717 3881 5.428457 TGATCATTATACTCCACCCTGTGTT 59.572 40.000 0.00 0.00 0.00 3.32
3776 3942 6.823689 TGAAGTTCTGTTAGGGCATATTTCTC 59.176 38.462 4.17 0.00 0.00 2.87
3778 3944 5.430089 AGTTCTGTTAGGGCATATTTCTCCT 59.570 40.000 0.00 0.00 0.00 3.69
3858 4025 2.260844 TGCTGAGACTGAAAACCCTG 57.739 50.000 0.00 0.00 0.00 4.45
3864 4031 5.396213 GCTGAGACTGAAAACCCTGATCTAT 60.396 44.000 0.00 0.00 0.00 1.98
3961 4128 6.920569 TTTGACGAAGAAGCTAAAGTTCTT 57.079 33.333 0.00 0.00 45.05 2.52
4528 4728 8.674263 ACATTTATCCTTAGAGAAATCTGCAG 57.326 34.615 7.63 7.63 40.97 4.41
4593 4794 8.962884 ATTTAGATTTTGTGCCTTCACTTTTT 57.037 26.923 0.00 0.00 43.49 1.94
4630 4831 6.974048 TCAATAATTTTCCAGATTGTCATGCG 59.026 34.615 0.00 0.00 32.33 4.73
4705 4910 5.763204 TGGAGACAGAATAAGTTGGTTTCAC 59.237 40.000 0.00 0.00 35.01 3.18
4741 4946 5.416083 CAATCATGATTTGGCTGTGATTGT 58.584 37.500 18.41 0.00 45.38 2.71
4746 4951 4.406456 TGATTTGGCTGTGATTGTTAGGT 58.594 39.130 0.00 0.00 0.00 3.08
4763 4968 5.361571 TGTTAGGTTTCACAGACTGACAGTA 59.638 40.000 8.41 0.00 0.00 2.74
4882 5096 6.970484 AGTATGTTTTCTGGTAAAACTGCAG 58.030 36.000 13.48 13.48 39.97 4.41
4985 5209 2.662791 CGCAAAACATCGACCTGAACAG 60.663 50.000 0.00 0.00 0.00 3.16
4996 5220 0.809385 CCTGAACAGAATGCTGCCAG 59.191 55.000 14.01 14.01 46.26 4.85
5059 5283 5.871524 ACAGCAGATGTTGAAGTATACAGTG 59.128 40.000 5.50 0.00 39.96 3.66
5067 5291 6.230472 TGTTGAAGTATACAGTGTTCAGCAT 58.770 36.000 14.17 0.00 35.86 3.79
5151 5375 3.965379 TGACATCTTTTGCATTGCCAT 57.035 38.095 6.12 0.00 0.00 4.40
5339 5564 6.094048 CCTCAGATGTTTCCGTATCAACATTT 59.906 38.462 0.00 0.00 42.46 2.32
5391 5616 3.725490 TCATGTGCATCTCTGACTATGC 58.275 45.455 11.47 11.47 46.92 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.527533 CCCGGACAGATTTTCGTATTCA 58.472 45.455 0.73 0.00 0.00 2.57
51 52 3.546815 CGCAGTCCAGAGTGAAGTTTTTG 60.547 47.826 6.67 0.00 33.67 2.44
63 64 4.401202 TCATCTACAATAACGCAGTCCAGA 59.599 41.667 0.00 0.00 45.00 3.86
110 111 1.067212 GAGTTCCACTGTGTCGTCACT 59.933 52.381 13.77 1.20 44.14 3.41
184 185 0.242825 CCTTAGACGCACAGTTCGGA 59.757 55.000 0.00 0.00 0.00 4.55
208 209 2.687566 CCCCGCCTCCTGTTACCT 60.688 66.667 0.00 0.00 0.00 3.08
244 245 2.511452 CCATCGAGAGGGCCCGAAT 61.511 63.158 18.44 6.05 38.36 3.34
424 426 3.011119 CGACTCTGTGTAACTCTAGCCT 58.989 50.000 0.00 0.00 38.04 4.58
431 434 4.139786 TCTGTAACCGACTCTGTGTAACT 58.860 43.478 0.00 0.00 38.04 2.24
459 462 6.264067 GCTTGGCAGTTAGGATATGAAGATTT 59.736 38.462 0.00 0.00 0.00 2.17
555 558 6.330278 GCTATATGCATATGTCGGACTGTTA 58.670 40.000 26.21 3.71 42.31 2.41
584 587 2.047830 GATTAAGGGGTCCTCGGACAT 58.952 52.381 17.21 1.67 46.20 3.06
621 624 0.753867 TACACAGGAGCGTTTGGACA 59.246 50.000 0.00 0.00 0.00 4.02
622 625 1.732259 CATACACAGGAGCGTTTGGAC 59.268 52.381 0.00 0.00 0.00 4.02
623 626 1.346395 ACATACACAGGAGCGTTTGGA 59.654 47.619 0.00 0.00 0.00 3.53
624 627 1.808411 ACATACACAGGAGCGTTTGG 58.192 50.000 0.00 0.00 0.00 3.28
625 628 3.896648 AAACATACACAGGAGCGTTTG 57.103 42.857 0.00 0.00 0.00 2.93
626 629 4.000988 CCTAAACATACACAGGAGCGTTT 58.999 43.478 0.00 0.00 0.00 3.60
627 630 3.596214 CCTAAACATACACAGGAGCGTT 58.404 45.455 0.00 0.00 0.00 4.84
628 631 2.093658 CCCTAAACATACACAGGAGCGT 60.094 50.000 0.00 0.00 0.00 5.07
629 632 2.550978 CCCTAAACATACACAGGAGCG 58.449 52.381 0.00 0.00 0.00 5.03
630 633 2.504175 TCCCCTAAACATACACAGGAGC 59.496 50.000 0.00 0.00 0.00 4.70
631 634 4.444876 CCATCCCCTAAACATACACAGGAG 60.445 50.000 0.00 0.00 0.00 3.69
632 635 3.458118 CCATCCCCTAAACATACACAGGA 59.542 47.826 0.00 0.00 0.00 3.86
633 636 3.458118 TCCATCCCCTAAACATACACAGG 59.542 47.826 0.00 0.00 0.00 4.00
634 637 4.771114 TCCATCCCCTAAACATACACAG 57.229 45.455 0.00 0.00 0.00 3.66
635 638 5.725551 AATCCATCCCCTAAACATACACA 57.274 39.130 0.00 0.00 0.00 3.72
636 639 5.221244 GCAAATCCATCCCCTAAACATACAC 60.221 44.000 0.00 0.00 0.00 2.90
637 640 4.892934 GCAAATCCATCCCCTAAACATACA 59.107 41.667 0.00 0.00 0.00 2.29
638 641 4.892934 TGCAAATCCATCCCCTAAACATAC 59.107 41.667 0.00 0.00 0.00 2.39
639 642 5.136068 TGCAAATCCATCCCCTAAACATA 57.864 39.130 0.00 0.00 0.00 2.29
640 643 3.992999 TGCAAATCCATCCCCTAAACAT 58.007 40.909 0.00 0.00 0.00 2.71
641 644 3.464720 TGCAAATCCATCCCCTAAACA 57.535 42.857 0.00 0.00 0.00 2.83
642 645 4.222810 ACTTTGCAAATCCATCCCCTAAAC 59.777 41.667 13.23 0.00 0.00 2.01
643 646 4.424842 ACTTTGCAAATCCATCCCCTAAA 58.575 39.130 13.23 0.00 0.00 1.85
644 647 4.023291 GACTTTGCAAATCCATCCCCTAA 58.977 43.478 13.23 0.00 0.00 2.69
645 648 3.269381 AGACTTTGCAAATCCATCCCCTA 59.731 43.478 13.23 0.00 0.00 3.53
646 649 2.043526 AGACTTTGCAAATCCATCCCCT 59.956 45.455 13.23 0.00 0.00 4.79
647 650 2.167075 CAGACTTTGCAAATCCATCCCC 59.833 50.000 13.23 0.00 0.00 4.81
648 651 2.167075 CCAGACTTTGCAAATCCATCCC 59.833 50.000 13.23 0.00 0.00 3.85
649 652 2.827921 ACCAGACTTTGCAAATCCATCC 59.172 45.455 13.23 0.00 0.00 3.51
650 653 4.240096 CAACCAGACTTTGCAAATCCATC 58.760 43.478 13.23 8.35 0.00 3.51
651 654 3.642848 ACAACCAGACTTTGCAAATCCAT 59.357 39.130 13.23 0.00 0.00 3.41
652 655 3.030291 ACAACCAGACTTTGCAAATCCA 58.970 40.909 13.23 0.00 0.00 3.41
653 656 3.733443 ACAACCAGACTTTGCAAATCC 57.267 42.857 13.23 7.54 0.00 3.01
654 657 5.689383 TCTACAACCAGACTTTGCAAATC 57.311 39.130 13.23 12.10 0.00 2.17
655 658 5.047802 CCATCTACAACCAGACTTTGCAAAT 60.048 40.000 13.23 3.03 0.00 2.32
656 659 4.278170 CCATCTACAACCAGACTTTGCAAA 59.722 41.667 12.14 12.14 0.00 3.68
657 660 3.820467 CCATCTACAACCAGACTTTGCAA 59.180 43.478 0.00 0.00 0.00 4.08
658 661 3.411446 CCATCTACAACCAGACTTTGCA 58.589 45.455 0.00 0.00 0.00 4.08
659 662 2.162408 GCCATCTACAACCAGACTTTGC 59.838 50.000 0.00 0.00 0.00 3.68
660 663 3.679389 AGCCATCTACAACCAGACTTTG 58.321 45.455 0.00 0.00 0.00 2.77
661 664 5.013183 ACTTAGCCATCTACAACCAGACTTT 59.987 40.000 0.00 0.00 0.00 2.66
662 665 4.532521 ACTTAGCCATCTACAACCAGACTT 59.467 41.667 0.00 0.00 0.00 3.01
663 666 4.097418 ACTTAGCCATCTACAACCAGACT 58.903 43.478 0.00 0.00 0.00 3.24
664 667 4.473477 ACTTAGCCATCTACAACCAGAC 57.527 45.455 0.00 0.00 0.00 3.51
665 668 5.269991 ACTACTTAGCCATCTACAACCAGA 58.730 41.667 0.00 0.00 0.00 3.86
666 669 5.599999 ACTACTTAGCCATCTACAACCAG 57.400 43.478 0.00 0.00 0.00 4.00
667 670 5.247564 ACAACTACTTAGCCATCTACAACCA 59.752 40.000 0.00 0.00 0.00 3.67
668 671 5.731591 ACAACTACTTAGCCATCTACAACC 58.268 41.667 0.00 0.00 0.00 3.77
669 672 8.943909 AATACAACTACTTAGCCATCTACAAC 57.056 34.615 0.00 0.00 0.00 3.32
670 673 9.953565 AAAATACAACTACTTAGCCATCTACAA 57.046 29.630 0.00 0.00 0.00 2.41
671 674 9.953565 AAAAATACAACTACTTAGCCATCTACA 57.046 29.630 0.00 0.00 0.00 2.74
674 677 9.740710 AAGAAAAATACAACTACTTAGCCATCT 57.259 29.630 0.00 0.00 0.00 2.90
677 680 9.959749 CAAAAGAAAAATACAACTACTTAGCCA 57.040 29.630 0.00 0.00 0.00 4.75
686 689 9.705290 ACTGTGTTTCAAAAGAAAAATACAACT 57.295 25.926 0.00 0.00 36.48 3.16
689 692 8.439286 GCAACTGTGTTTCAAAAGAAAAATACA 58.561 29.630 0.00 0.00 35.14 2.29
690 693 8.439286 TGCAACTGTGTTTCAAAAGAAAAATAC 58.561 29.630 0.00 0.00 0.00 1.89
691 694 8.539770 TGCAACTGTGTTTCAAAAGAAAAATA 57.460 26.923 0.00 0.00 0.00 1.40
692 695 7.432350 TGCAACTGTGTTTCAAAAGAAAAAT 57.568 28.000 0.00 0.00 0.00 1.82
693 696 6.851222 TGCAACTGTGTTTCAAAAGAAAAA 57.149 29.167 0.00 0.00 0.00 1.94
694 697 6.851222 TTGCAACTGTGTTTCAAAAGAAAA 57.149 29.167 0.00 0.00 0.00 2.29
695 698 6.851222 TTTGCAACTGTGTTTCAAAAGAAA 57.149 29.167 0.00 0.00 0.00 2.52
696 699 6.851222 TTTTGCAACTGTGTTTCAAAAGAA 57.149 29.167 13.71 0.00 33.39 2.52
699 702 6.851222 TTCTTTTGCAACTGTGTTTCAAAA 57.149 29.167 15.73 15.73 35.92 2.44
709 712 5.947503 TTCAACGATTTCTTTTGCAACTG 57.052 34.783 0.00 0.00 0.00 3.16
779 784 5.407407 TGAGTTTTGGAGGATAGACTGTC 57.593 43.478 0.00 0.00 0.00 3.51
783 788 7.556844 TCACTTATGAGTTTTGGAGGATAGAC 58.443 38.462 0.00 0.00 32.54 2.59
797 802 8.503458 CTTGATTCAAAGGATCACTTATGAGT 57.497 34.615 0.01 0.00 38.85 3.41
1081 1191 3.070018 CGATGTTCTTCTTCTTGGTGCT 58.930 45.455 0.00 0.00 0.00 4.40
1127 1237 2.046217 GGGAGTTTGCGGGAGGTC 60.046 66.667 0.00 0.00 0.00 3.85
1151 1261 3.017442 CCTCGAATGAGACACTGGACTA 58.983 50.000 0.00 0.00 45.57 2.59
1241 1351 2.435938 GCGACCTGGAATGCGGAA 60.436 61.111 0.00 0.00 0.00 4.30
1519 1648 0.320421 TTCCCGTAAGCAGCAGTGAC 60.320 55.000 0.00 0.00 0.00 3.67
1572 1701 2.673368 CAGATTTCTGGACTTACCGCAC 59.327 50.000 0.00 0.00 42.61 5.34
1575 1704 4.322049 ACAGACAGATTTCTGGACTTACCG 60.322 45.833 11.99 2.87 46.38 4.02
1635 1764 3.503827 ATTGTTCATCATGCAGCACAG 57.496 42.857 0.00 0.00 0.00 3.66
1751 1880 9.582431 GCAAACATGTATAGTGAACTAAGTAGA 57.418 33.333 0.00 0.00 31.39 2.59
1804 1933 6.790232 AAAAGACCTGATTTGGTTTTGAGA 57.210 33.333 0.00 0.00 41.00 3.27
1874 2003 6.770785 GGATTCCATAACTATTGCAACCACTA 59.229 38.462 0.00 0.00 0.00 2.74
1875 2004 5.594317 GGATTCCATAACTATTGCAACCACT 59.406 40.000 0.00 0.00 0.00 4.00
1876 2005 5.359576 TGGATTCCATAACTATTGCAACCAC 59.640 40.000 0.00 0.00 0.00 4.16
1979 2112 1.982395 TCGGTGGCAACTCTCCGAT 60.982 57.895 11.61 0.00 44.69 4.18
1980 2113 2.599281 TCGGTGGCAACTCTCCGA 60.599 61.111 11.61 11.61 46.22 4.55
1982 2115 0.460987 CTGATCGGTGGCAACTCTCC 60.461 60.000 0.00 0.00 37.61 3.71
2001 2135 2.967362 TGGTTGTGTATGGACATCGAC 58.033 47.619 0.00 0.00 38.04 4.20
2067 2201 7.009723 CAGAATCAGATCTAGCATGAATCATCG 59.990 40.741 0.00 0.00 0.00 3.84
2125 2262 1.209747 CCCCTAAGCTTGACTGGTACC 59.790 57.143 9.86 4.43 0.00 3.34
2248 2385 3.949754 TGTACCTGGTATACAAGGAGACG 59.050 47.826 29.90 6.16 29.59 4.18
2271 2408 7.398904 AGGCAACAAACTTGGGTGTATATTAAT 59.601 33.333 0.00 0.00 41.41 1.40
2679 2818 5.932303 ACGAATCCCGAAATGATGGTTATAG 59.068 40.000 0.00 0.00 41.76 1.31
2702 2841 9.508567 GAGCATCTATTTTCATTACCAAGAAAC 57.491 33.333 0.00 0.00 33.82 2.78
2776 2915 0.962489 AGTCCTCACGAACAGACAGG 59.038 55.000 0.00 0.00 0.00 4.00
2799 2940 5.609423 TCCCATGAAAAGTTTCCAATGTTG 58.391 37.500 0.00 0.00 36.36 3.33
2847 2988 9.685828 TCCAGTAAATTAGCAAACAAATAACAC 57.314 29.630 0.00 0.00 0.00 3.32
2882 3023 1.063567 ACTAACCCAACCCTTGCACAA 60.064 47.619 0.00 0.00 0.00 3.33
2990 3131 7.987458 TGGTGCCTACAAACAAAATGATAAAAA 59.013 29.630 0.00 0.00 0.00 1.94
3163 3304 7.060600 TCTCTGTGAATTGTAAAGCGTAATG 57.939 36.000 0.00 0.00 0.00 1.90
3355 3496 2.530958 TTACTACCTTGGGCGCCAGC 62.531 60.000 30.85 12.89 44.18 4.85
3470 3618 7.496529 TCCTAGTGAATTTTGACAAAGACTG 57.503 36.000 0.10 0.00 0.00 3.51
3679 3843 6.971726 ATAATGATCAGGTGAATGCAACAT 57.028 33.333 0.09 0.00 32.84 2.71
3700 3864 6.499350 ACTTTAGAAACACAGGGTGGAGTATA 59.501 38.462 1.07 0.00 37.94 1.47
3701 3865 5.309806 ACTTTAGAAACACAGGGTGGAGTAT 59.690 40.000 1.07 0.00 37.94 2.12
3919 4086 0.613292 ATGTCAGCCAGGACTCGTCT 60.613 55.000 0.00 0.00 38.61 4.18
3961 4128 7.939039 AGAATCAGAAAACTCACCTTGTTATGA 59.061 33.333 0.00 0.00 0.00 2.15
4158 4325 7.318141 AGAATAGTATTTCGTTTTCGTCTCCA 58.682 34.615 0.00 0.00 44.46 3.86
4705 4910 7.381408 CCAAATCATGATTGAATTCTCGAATGG 59.619 37.037 21.39 15.43 34.96 3.16
4741 4946 5.831525 TCTACTGTCAGTCTGTGAAACCTAA 59.168 40.000 9.26 0.00 36.74 2.69
4746 4951 4.099419 TGCTTCTACTGTCAGTCTGTGAAA 59.901 41.667 9.26 0.00 36.74 2.69
4763 4968 1.067295 TGTCACCCCTCATTGCTTCT 58.933 50.000 0.00 0.00 0.00 2.85
4882 5096 9.391006 TGTGATTCTAAATAGGTGAATGGTTAC 57.609 33.333 0.00 0.00 31.49 2.50
4985 5209 3.441572 AGTTGTAACATCTGGCAGCATTC 59.558 43.478 10.34 0.00 0.00 2.67
5046 5270 7.744087 AAAATGCTGAACACTGTATACTTCA 57.256 32.000 4.17 4.94 0.00 3.02
5059 5283 5.126396 AGTCCTTGCTAAAAATGCTGAAC 57.874 39.130 0.00 0.00 0.00 3.18
5067 5291 7.817418 ACATGAAGTTAGTCCTTGCTAAAAA 57.183 32.000 0.00 0.00 33.34 1.94
5339 5564 5.554437 TGTTTGGTGTACCTATGTCTTCA 57.446 39.130 2.32 0.00 36.82 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.